Step 2. (Optional) Remove existing IDs from VCF file

You may skip this step if you would like to preserve existing IDs in your VCF file. Otherwise, the existing variant IDs can be removed from the VCF file using the bcftools annotate tool with the –remove option.

It looks like there is something wrong with the header of your VCF files. You can extract the header using `bcftools view –header-only`, fix it in any text editor, and replace headers in the VCF files using `bcftools reheader`.